* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background."

* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background."

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* [http://www.bioconductor.org/packages/release/bioc/html/gage.html GAGE] is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity ([http://www.biomedcentral.com/1471-2105/10/161 paper]). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general.

* [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] R/Bioconductor tool for pathway based data integration and visualization, easy to integrate in pathway analysis workflows. [http://pathview.r-forge.r-project.org/ R-Forge]has an overview with some nice example plots. The work has been published in [http://bioinformatics.oxfordjournals.org/content/early/2013/06/11/bioinformatics.btt285.full Bioinformatics].

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* [http://bioconductor.org/packages/release/bioc/html/pathview.html Pathview] R/Bioconductor tool for pathway based data integration and visualization, easy to integrate in pathway analysis [http://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf workflows]. [http://pathview.r-forge.r-project.org/ R-Forge]has an overview with some nice example plots. The work has been published in [http://bioinformatics.oxfordjournals.org/content/29/14/1830.full Bioinformatics].

=Protein interactions=

=Protein interactions=

Current revision

After determining a list of genes involved in a given biological process the next step is to map these genes to known pathways/Gene Ontology terms and determine i.e. which pathways are overrepresented in a given set of genes.

GSEA withMSigDB "Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states"

ErmineJ "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background."

GAGE is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity (paper). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general. Tutorials describe both RNA-Seq and microarray data analysis workflows.

Pathway/graph visualisation

Pathview R/Bioconductor tool for pathway based data integration and visualization, easy to integrate in pathway analysis workflows. R-Forgehas an overview with some nice example plots. The work has been published in Bioinformatics.